Mapping of ISGC SNP chip probes

Ovine SNP chips created by the International Sheep Genomics Consortium (ISGC, https://sheephapmap.org/) were mapped onto reference genomes. Results are reported per chip and include SNP_name, chrom, pos, ref_alt, flag, rsID.<br>Probe sequences were taken from the Illumina manifests (ISGC_SheepLD2015_15K_20003262_A1, OvineSNP50_B, SheepHD_AgResearch_Cons_15041608_A) and mapped onto the Oarv3.1 (GCF_000298735.1) and the Rambouillet version 2 (GCA_016772045.1) reference genomes using bwa mem v0.7.17-r1188 with default settings. Only SNPs were mapped, indels were ignored.<br>For each SNP a probe pair was constructed by using AlleleA_ProbeSeq and appending either the reference or the alternative allele. <br>Only probe pairs where accepted that passed following filters.-both probes have no alternative mappings<br>-both probes are mapped<br>-one probe is mapped with 0 mismatches<br>-both probes are not multi-mapped<br>-no indels were allowed<br>-both probes had to map in the same orientation<br>-both probes had to map to the same position<br>-mapped probes had between them exactly 1 mismatch, the SNP.<br>Mapped SNPs got assigned to rsIDs via their Oarv3.1 position (ftp://ftp.ensembl.org/pub/release-100/variation/vcf/ovis_aries/ovis_aries.vcf.gz).<br><br><br><br>Any data shared here is without warranty
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